Secondary structure and small RNA-seq evidence for dme-mir-4985

Legend:maturestarmismatch

12 Drosophila species corrected alignment

Species Coordinate Alignment
dm3 chr2R:20181738-20181869 + ATAAAAAGTATGTCACT------------------T-GGGG-GCGCTGCACT---------GGCATTGAAA-AGTGAA------TTACATTGATCGTGACATGGGAATGGAAAATGTCGCCG-----------------------------------------------------------------------------------------------------------------------------------------------AGCCATGTAAATCGTTTGGCCTACCCGTCTACCA-GCCAACC----AACCA
droSim1 chr2R:18643325-18643449 + ATAAAAAGTATGTCACT---------------TGGTG-GGG-GCGCTGCACT---------GGCATTGAAA-AGTGAA------TTACATTGATCGTGACATGGGGATGGAAAATGCCGCCG-----------------------------------------------------------------------------------------------------------------------------------------------AGCCATGTAAATCGATTG---------AAGGCC-C-GTGGCC----AACCA
droSec1 super_23:61187-61303 + ATAAAAAGTATGTCACT---------------TGGTG-GGG-GCGCTGCACT---------GGCATTGAAA-AGTGAA------TTACATTGATCGTGACATGGGGATGGAAAATGTCGCCG-----------------------------------------------------------------------------------------------------------------------------------------------AGCCATGTAAATCGATTG---------AAGGCC-C-GTG------------
droYak2 chr2R:20147877-20148015 + ATAAAAAGTATGTCACT------------------G-GGGG-GCGCTGCACT---------GGCACTGAAA-AGTGAA------TTACATTGATCGTGACATGGGGATGCGAAATGTCGCCAAACGAAAAA----ATAAATCA----------------------------------------------------TAG------------------------------------------------------------------------TGTAACTCGTTTG---------AAGGCCACACCAACT----AGTAA
droEre2 scaffold_4845:21546843-21546980 + ATAAAAAGTATGTCACT---------------A----GGGGGCTTCTGCACT---------GGCATTGAAA-AGTGAA------TTACATTGATCGTGACATGGGGATGGAAAATGTCGCCGCACAAAAAA--------AGTG----------------------------------------------------TAG------------------------------------------------------------------------TGTAAATCGTTTG---------AAGGCC-C-ATGGCCAACCAACCG
droAna3 scaffold_13266:14229911-14230049 - AAAAAAAGTATGTCACA---------------C--TG-GGG-GAACTGCACT---------GACATTGAAAAACTGAA------TTACATTGGACGGTGGATGGG-------------------------------------------TGGACTGATGGACTGATGGACTGACAGCCA-------------------------------------------------------CGATCATC--------ACTAGCGTCGCAGTTAAGTTATGTAA-------------------------------------ACCG
dp4 chr3:18492568-18492741 - GTAAAAAGTATGTCAGAGAAGAGAAGAGAACACAGTGGGCG-CTGCTGCACT---------GACATTGAAA-AGTGAA------TTGCATTGATCATGACGGGGGGTTGA-------CGCTG-------------------------------------------------ACTGCCACGAACCGCTCAGAACAATAGTGTAAATGTGGAATAATGCTCG--------------------------------------------------TAGAAC-CCATTC---------G----CA-GTCCATG----GGCTG
droPer1 super_45:328754-328870 - GTGAAATGTATTTGAAA---------------------------------CG---------AGTAACGGAA-ATTGCA------TTATTTCAATTACAAA-----------------------------------TCCAATGAGAGGGAGAGGG-------ACAGGGA----C---------------------------------------------AGGG-------------------------------------------ACCCAGCACAA-----------CCCTAGGAGCCA-GCCAGCC----AGCCA
droWil1 scaffold_180949:4063354-4063494 - ATTGAGGGCGTGATTTA------------------TG-CCC-GATCTACCCC---------ATCATTTAAT-GTTAAAGACAATGCTAATTGGCCATTAAAATAGGCCG-----------CA------------------------ACAGACAC-------AAATAGT----T---------------------------------------------TGGGACCTA------AAATCAAA-------------------------------------------GCCAACCGACCACCA-GCCAACC----AGCCA
droVir3 scaffold_12875:7276052-7276211 + GG----------------------------------------GCGCTGCATTTGCCAGGCCAGAGTTAAAA-AGTGAA------TTGAATTGGCCGCTTGATTGA-------------------------------------------CAG-CCGACGGGCTGA-------------------------------------ATATGTGCAGCAATGCCAACAAATCGATGCCAAAGTCAGTGTCAGTCCCACGTAATCGACAATCAGTTATTTAC-----------------------A-TACGAGC----CACAA
droMoj3 scaffold_6473:1699609-1699741 - ATAATCTATTAGTTATT---------------TAATA-TAT-GT------------------------------CAATCATTCAGCCACTCAATCATTAA-----------------------------------GTTAATCAACGAGTAACTC-------AATCAGT----C---------------------------------------------AGTCATTCAGTGCCTCAATCGTT----------------------------------------AAGTCTTCCAATAAGTCA-CTCAATC----AGTCA
droGri2 scaffold_15203:4626832-4626941 - GCCCATGCCA--------------------------------------------------------TAAAA-AGAGTT------TTGAACTAATCTTAAGCAGGCAGCGCAAATCGCTATAAATCAG-CTTTCTATTCTT--------------------------------------------------------TG------------------------------------------------------------------------TT---------TTGCCCCACTGTGCACCA-GCCAGCC----AGCCA

Reduced alignment with Hairpin orthologs

Species Coordinate Alignment
dm3 chr2R:20181738-20181869 + ATAAAAAGTATGTCACTTGGGGGCGCTGCACTGGCATTGAAAAGTGAATTACATTGATCGTGACATGGGAATGGAAAATGTCGCCGAGCCATGTAAATCGTTTGGCCTACCCGTCTACCAGCCAACCAACCA

Small RNA-sequencing read pileup

Species Read pileup
droSim1
ATAAAAAGTATGTCA---------------CTTGGTGG-GGGCGCTGCACTGGCATTGAAAAGTGAATTACATTGATCGTGACATGGGGATGGAAAATGCCGCCGAGCCATGTAAAT-------------------------------------------CGATTG-------------AAGGCCCGTGGCCAACCASizeHit CountTotal NormTotalGSM343915
Embryo
No Reads
dp4
GTAAAAAGTATGTCAGAGAAGAGAAGAGAACACAGTGGGCGCTGCTGCACTGACATTGAAAAGTGAATTGCATTGATCATGACGGGGGGTTG-------ACGCTGACTGCCACGAACCGCTCAGAACAATAGTGTAAATGTGGAATAATGCTCGTAGAACCCATTC-------------GCAGTCCATG---GGCTGSizeHit CountTotal NormTotalGSM343916
Embryo		GSM444067
Head
No Reads

Secondary Structure

dm3

dG=-15.2,  p-value=0.009901 dG=-15.2,  p-value=0.009901 dG=-15.0,  p-value=0.009901 dG=-15.0,  p-value=0.009901 dG=-14.5,  p-value=0.009901

droSim1

dG=-15.0,  p-value=0.009901 dG=-14.8,  p-value=0.009901 dG=-14.4,  p-value=0.009901 dG=-14.3,  p-value=0.009901 dG=-14.1,  p-value=0.009901

droSec1

dG=-14.7,  p-value=0.009901 dG=-14.7,  p-value=0.009901 dG=-14.4,  p-value=0.009901 dG=-14.4,  p-value=0.009901 dG=-14.0,  p-value=0.009901

droYak2

dG=-12.7,  p-value=0.009901 dG=-12.5,  p-value=0.009901 dG=-12.5,  p-value=0.009901 dG=-12.3,  p-value=0.009901 dG=-12.2,  p-value=0.009901

droEre2

dG=-14.1,  p-value=0.009901 dG=-13.9,  p-value=0.009901 dG=-13.9,  p-value=0.009901 dG=-13.9,  p-value=0.009901 dG=-13.7,  p-value=0.009901 dG=-12.8,  p-value=0.009901

droAna3

dG=-22.7,  p-value=0.009901 dG=-22.6,  p-value=0.009901 dG=-22.4,  p-value=0.009901 dG=-22.3,  p-value=0.009901 dG=-22.2,  p-value=0.009901

dp4

dG=-16.7,  p-value=0.009901 dG=-16.3,  p-value=0.009901 dG=-16.3,  p-value=0.009901 dG=-16.2,  p-value=0.009901 dG=-16.2,  p-value=0.009901 dG=-15.4,  p-value=0.009901

droPer1

dG=-6.9,  p-value=0.009901 dG=-6.1,  p-value=0.009901 dG=-5.9,  p-value=0.009901 dG=-2.8,  p-value=0.009901

droWil1

dG=-10.4,  p-value=0.009901 dG=-10.2,  p-value=0.009901 dG=-9.9,  p-value=0.009901 dG=-9.7,  p-value=0.009901 dG=-9.6,  p-value=0.009901 dG=-8.2,  p-value=0.009901

droVir3

dG=-27.7,  p-value=0.009901 dG=-27.3,  p-value=0.009901 dG=-27.2,  p-value=0.009901 dG=-27.2,  p-value=0.009901 dG=-27.1,  p-value=0.009901 dG=-24.4,  p-value=0.009901

droMoj3

dG=-3.4,  p-value=0.009901 dG=-2.9,  p-value=0.009901 dG=-2.9,  p-value=0.009901 dG=-2.6,  p-value=0.009901 dG=-2.6,  p-value=0.009901

droGri2

dG=-8.1,  p-value=0.009901 dG=-7.9,  p-value=0.009901 dG=-7.8,  p-value=0.009901 dG=-7.5,  p-value=0.009901 dG=-7.5,  p-value=0.009901

Generated: 03/07/2013 at 06:53 PM